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A multiple metal(loid)-resistant strain Comamonas testosteroni S44 was isolated from mining waste soil. This bacterium exhibited a high Zn2+ resistant level with a minimal inhibitory concentration (MIC) of 10 mM. To understand the molecular basis for the high zinc resistance，whole genome sequencing was performed and showed large number of genes encoding putative metal(loid) resistance proteins，mobile genetic elements (MGEs)，recent gene transposition，gene duplication and other events pointing to a mobile genome in the process of adaptation to a metal(loid)-contaminated environment. Particularly，a total of nine putative Zn2+ transporters (four putative zntA operons encoding P-type ATPase pumps and five czc operons encoding RND-transport efflux proteins) were identified in the draft genome sequence.